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<title>Sequence Details</title>
<h1>Sequence Details</h1>
Some details:
<ol>
<li>Best ORF: shows the RF (reading frame) and coordinates. A '*' indicates a missing start or stop. 
<li>DB hits table columns: The E-value, Percent, AlignLen, QueryStart and QueryEnd are from the first BLAST results for
 the hit. Note that the AlignLen is in protein coordinates, whereas the QueryStart and QueryEnd are nucleotide coordinates (for transcripts). For example:
<table border=1>
<tr><td>&nbsp;<td>&nbsp; <td>Percent <td>Align<td>Mis-    <td>Gap <td>Query<td>Query<td>Subj <td>Subj<td>&nbsp;
<tr><td>Query <td>Subject<td>Identity<td>Len  <td>matches<td>Open<td>Start<td>End  <td>Start<td>End<td>E-value
<tr><td>OlD_026<td>A2WSF2<td>32.96   <td>358  <td>162     <td>11  <td>1    <td>849 <td>131  <td>485<td>1e-23
</table>
</pre>
</ol>
The options in the top row change the content of the panel. The first two options of the second
row change the content of the initial 'overview' panel.
<h3>Show (first row, left)</h3>
<ul>
<li>Overview: the initial page of sequence details.
<li>Show All GOs or from selected hit: If a hit is selected in the DB hits table, only the GOs for that hit are shown; otherwise, all GOs for all hits are shown. The whole tree is shown. 
<br>Note: If a hit is selected and you want to unselect it, select the hit again with the Ctrl key pressed down.
<li>Show Sequence (if no alignment) or Show Alignment (if assembled dataset).
<li>Show SNPs (if assembled dataset): shows a table of the SNPs.
<li>Align DB hits - on: shows a view from the 'Align DB Hits'.
</ul>

<h3>Align DB hits (first row, right)</h3>
The hits are aligned using the reading frame of the respective BLAST HSP.
<ul>
<li>Align Best Hit: aligns the BestEval and BestAnno (which may be the same).
<li>Align DB hit table contents: align whatever sequences are in the DB hits table (which can
be changed with the "List DB hits").
<li>Align selected hit(s): select one or more hits from the DB hits table to be aligned.
<li>Align selected hit(s) in all frames: this will take awhile, so you should only select one.
</ul>

<h3>Show raw counts, RPKM or replicas (second row, left)</h3>
Has the options: Show >0 counts, Show >0 RPKM, Show all counts, Show all RPKM, Show replicas (if there are replicas on the input).
(Note, the first two options help to reduce the display in case there are many libraries.)

<h3>List DB hits (second row, middle)</h3>
Changes the set of hits listed in the overview table.
<ul>
<li>best eval & anno.
<ul>
<li>BestEval: the hit with the best evalue (though it may be 'almost' the best evalue
if there is a hit with a more informative description and the evalue is almost as good).
<li>BestAnno: the hit with best evalue and informative description, which is one that 
does not have terms like "uncharacterized protein".
<li>The BestAnno and BestEval may be the same. They may not be in the list of "best per annoDB".
</ul>
<li>best per annoDB: in preprocessing, the sequences in the database are generally blasted against
one or more databases, where each is referred to as an 'annoDB'. For example, the sequences
may have been blasted against SwissProt Plants and TrEMBL Plants taxonomic databases. So the best
hit for each is listed.
<li>Minimal overlap: a set of hits that represent the regions of DB hit overlap based on BLAST HSPs 
<li>Unique gene rep: (1) ignore putative, hypothetical and predicted, (2) remove last character of description as often a number or letter.
<li>Unique species: lists one of each species that was hit
</ul>

<h3>Copy/Export (second row, right)</h3>
The "Copy/Export" is a menu of options to copy content to the clipboard (to be copied elsewhere)
and options to write information to file. <i>The Copy options do not always work through VNC,
and for large tables, it is sometime necessary to select 'Cntl-C' to complete it.</i>
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